A lot of the molecules in our bodies like to hang out with water & will happily put on a water-coat (dissolve in water). We call such water-loving molecules hydrophilic. Other molecules, lipids like oils & fats, water hates and thus excludes – we call these hydrophobic. But it’s not like all molecules are hydrophobic OR hydrophilic. Some molecules are BOTH – one part is hydrophobic and one part is hydrophilic – we call such molecules amphiphilic (aka amphipathic) and they include soaps, detergents, and phospholipids. 

text adapted from past posts, video new

Soaps & detergents have a hydrophilic head that water’s cool with and a hydrophobic tail that water rejects. So these molecules orient themselves so that those hydrophobic tails huddle together with the heads sticking out to interact with the water. Their heads are “bulkier” so when they do  this, they forms spheres called micelles with room inside for other hydrophobes to reside – if there’s greasy (hydrophobic) gunk present, micelles can form around it, coating that gunk with their hydrophobic tails facing the gunk & hydrophilic heads facing the water. So now, instead of stuck-on gunk, you have a soluble “packet” of gunk you can wash away. They’re also great for reducing surface tension (acting as a surfactant) letting you blow bubbles! As I’ll talk about later, detergents are just “artificial soaps” and we can use them in the lab frequently.

Phospholipids are similar to soaps and detergents in that they are amphiphilic because they have hydrophilic heads & hydrophobic tails, but they have multiple tails. They’re bulkier & it’s harder for them to coordinate w/one another to form little spheres – instead they arrange themselves into phospholipid bilayers, which are like sandwiches with the tails as the “peanut butter” and the heads as the breads. This configuration helps them cordon off the watery inside of the particle from the (often watery) outside world.⠀

Phospholipids, the molecules making up cellular membranes, are similar to soaps & detergents in that they are amphiphilic because they have hydrophilic heads & hydrophobic tails, but they have 2 tails. They’re bulkier & it’s harder for them to coordinate w/one another to form little spheres – instead they arrange themselves into bilayer “sandwiches” with the tails in the middle.

Now that we’ve gotten the general introductions out of the way, let’s look in depth at what’s going on…

What makes something hydrophilic? Charge or partial charge. You see, water, H₂O, might “look” neutral – you don’t see any + or – signs indicating it’s an ion (charged molecule) – and it is neutral overall,  but its charge is unevenly distributed. ⠀

To understand why, you need to know a little about where that charge comes from. Molecules are made up of atoms and atoms are made up of charged parts (positive protons and negative electrons) and neutral parts (neutrons). Atoms can bond to each other by sharing electrons in covalent bonds, and some atoms can donate or take electrons from other atoms. All the while, the number of protons remains the same (and it’s this proton number that defines an element (e.g. oxygen has 8 protons and will always have 8 protons)). The reason some molecules are charged is that they have uneven numbers of protons and electrons. An excess of electrons gives you a negatively-charged molecule (anion) – too few electrons and you get a positively-charged molecule (cation).⠀

Some molecules, like water, have an even number of protons and electrons, so they’re neutral overall, but the electrons like to hang out at certain parts more than others so those parts become partly negative and the other parts, where the electrons spend less time, become partly positive. ⠀

Oxygen is more electron-hogging (electronegative) than hydrogen, so the O in H₂O is partly negative (δ⁻) and the H’s partly positive (δ⁺). This creates a charge imbalance called a dipole, and we call molecules with dipoles polar. Because opposite charges attract, the O will be attracted to positive things – either fully-charged anions or molecules with dipoles (even other water molecules which gives you things like the surface tension that makes water “sticky”).⠀

Since our bodies are so watery, biochemicals are typically “designed” to live in a watery environment (an exception being the membranes & molecules that reside in them). For example, nucleic acids (DNA & RNA) are very hydrophilic because they have negatively-charged phosphates in their backbone as well as polar sugars.

Proteins, which are made up of amino acid building blocks have some hydrophilic parts, but they also have some hydrophobic parts – some of the amino acids have hydrophilic side chains (their unique part), making them happy to hang out with water. But other amino acids have hydrophobic side chains. Hydrophobic molecules are ones that avoid water. Don’t let the name scare you off – water doesn’t even “scare” off these molecules despite the “phobia” in the name. The molecules aren’t really “scared” of water – the water just doesn’t want to hang out with them and tries to minimize its contact with them in favor of maximizing its contact with other water molecules.⠀

The reason for this is that hydrophobic molecules (or at least the hydrophobic parts of molecules (it’s not all or nothing)) don’t have charges (full or partial ones) so no one stands to gain from a hydrophobe-water interaction. There are no charge attractions possible and water doesn’t want to give up the attractions it can find elsewhere to hang out with something that can’t make it happy. And the hydrophobic molecules have no desire to hang out around charge, so, as water gangs up around them, they “team up” to reduce their contact with water through so-called hydrophobic interactions. This is referred to as the water exclusion effect, and it’s actually the driving force behind protein folding!⠀

I said hydrophobes were “really boring” attractiveness-wise, but I also mentioned “hydrophobic interactions”… it’s not a contradiction, because even hydrophones can (temporarily) “turn on the charm”…

Electrons move about randomly so if a lot happen to be in one place, they can induce a shift in the electrons in the molecules next to them (which will want to get away from the negativity, leaving the area partly positive & thus attractive to the first) -> leads to a chain reaction of little shifts so you get induced dipole interactions. Lots of temporary, weak attractions combine to give you a stronger attraction. These are sometimes called van der Waals (vdw) interactions. and you can learn more about them here: http://bit.ly/2C6oQIT

Lipids are largely non-polar because they’re made from chains of carbon and hydrogen, which share electrons pretty fairly. This makes them pretty “boring” as is – they lack so-called “functional groups” that give them “special powers” like enabling them to react and/or combine with other molecules. So, instead of just plain chains, the “starter kit” for a lipid is typically a “fatty acid.” It’s a hydrocarbon chain with a carboxylic acid (C=O)-OH group stuck onto the end. That carboxylic acid *is* reactive, so now you can make different things from these fatty acids. (you can think of the carboxylic acid kinda like putting the bump on a LEGO – speaking of which, not a paid endorsement but there’s now a LEGO wars reality TV show!)⠀more here:  https://bit.ly/lipidlove

If you take pure hydrocarbons & water, they won’t mix – they’ll split into a lipid layer & a water layer. This is the basis of many organic chemistry extraction techniques because lipid-soluble things will side with the lipid & water-soluble things will side with the water. We take advantage of this sort of thing in RNA extraction/purification: http://bit.ly/trizolRNAextraction  

That wouldn’t be very helpful in your body though. Instead, we need things that can get along with both & give molecules a chance to move between them. Molecules with both hydrophilic & hydrophobic parts are called amphiphilic (aka amphipathic) and they include things like soaps, detergent, and phospholipids. ⠀

Common examples are surfactants like soap & detergents (artificial soaps) – these SURFace ACTing agENTS accumulate at the water’s SURFace and ACT to to change the surface’s properties, such as lowering the water’s surface tension (how sticky the water is to other water molecules) – by interfering with these water-water bonds, it gives other molecules a chance to hang out with water -> helps things dissolve⠀

At low concentrations, they’ll spread out throughout the  water, but when the concentration gets high enough, they’ll “team up” to hide from water, creating micelles – spheres with the tails in the middle, away from water, & heads on the water-facing side. A lot of the gunk you want to get off pots & pans is lipid-y – it can get dissolved in the surfactant tails and trapped in the micelle center, allowing you to wash it off. Similarly, they can break apart viral membranes, killing viruses like the SARS-Cov-2 virus that causes Covid-9 (“coronavirus”) and clean up after themselves. http://bit.ly/detergentsandsoaps 

But In order to do this, there needs to be enough of the surfactant molecules to make a sphere and they have to be able to find one another. So the concentration of surfactant helps determine when micelles will form. The “tipping point” concentration is called the Critical Micelle Concentration (CMC) and different surfactants have different ones – you don’t really have to worry about this in day to day life, where you want to be above the CMC. but it is something to keep in mind if you’re using detergents in the lab – often, to help keep things soluble, scientists will add a really low concentration of detergent (like Tween-20 or Triton X-100) – and it’s important here that you remain *below* the CMC so you don’t cordon off molecules within your solution.⠀

Soaps are effective against lipid-coated viruses in part because they look similar enough to the lipids making up the viral membrane to wedge their way in. That viral membrane comes from budding out of our cells, picking up “our membranes” so both are made up of a phospholipid bilayer (kinda like a molecular sandwich)⠀

Our own cells, including those of our skin, are also surrounded by phospholipid membranes – so you might wonder why soap doesn’t just dissolve us in the process – thankfully, our skin is protected by a thick layer of dead skin cells called the stratum corneum.

A closer look at soaps and detergents at the molecular level…⠀

First – the terminology – detergents are just “artificial” versions of soaps. This doesn’t mean they’re bad, it just means they’ve been synthesized, which offers opportunities for molecular “enhancement.”⠀

Both have a hydrophobic tail made up of a long hydrocarbon chain – the linked-together hydrogens (H’s) and carbons (C’s) & C share electrons equally, giving you a long nonpolar part (how long depends on how many Cs & Hs, and the length helps determine “latherability”)⠀

Where soaps and detergents diverge is in the hydrophilic heads.  Soaps are derived from natural fatty acids, so they all have same head (carboxylate, which is ➖). But detergents can be synthesized to have different heads, which can be ➖ or➕, or even neutral but polar (nonionic detergents)⠀

Different detergents form micelles with different numbers of detergent molecules – the aggregation number  – and in order for micelles to form you have to have enough detergent molecules for them to be able to find one another and team up – the concentration at which this becomes likely is the Critical Micelle Concentration (CMC) – it depends on the molecular makeup of the detergent (e.g. less lipophilic detergents are more less desperate to avoid water by hanging out together and minimizing their exposure so you have to get more of them together to “convince them” to → higher CMC.)⠀

Detergents are used frequently in the lab, and lab-by detergents often have cool names, like “Tween” and “Triton.” More on those in a second, but I’ve gotta start by talking about the most “famous” detergent of them all – Sodium DodecylSulfate – the SDS behind SDS-PAGE!

Similarly to how soaps and detergents can sneak into cell membranes, some can slither into proteins & denature (unfold them) and others can break up protein-protein interactions but leave the proteins folded. SDS is a really harsh detergent – and that harshness is great for SDS-PAGE because it unfolds proteins so that you can separate proteins based only on their “length” instead of their shape. By “harsh” I mean that SDS actually denatures (unfolds) proteins, whereas milder detergents like Tween-20 leave them be, just disrupt proteins’ interactions with one another. Mild detergents like Tween-20 are often used at low concentrations designed to break up weak, non-specific interactions, but not denature (unfold) proteins and not “outcompete” specific interactions, whereas we use harsh detergents like SDS when we want to denature them. 

SDS is negatively charged (anionic) – which is one of the primary reasons we use it for SDS-PAGE, a technique to separate proteins by size by sending them traveling through a PolyAcrylamide Gel mesh using Electrophoresis (bigger proteins get tangled up more so travel slower). The SDS is crucial to this technique for a couple of reasons: when SDS unfolds & coats proteins, it coats them with negative charge. And that negative charge gives us a way to direct them by putting a positive charge to “bribe them” to go where we want them to go (towards the bottom of the gel in SDS-PAGE. The negative charge also makes the proteins stay unfolded because negative charges repel each other. Once the protein’s unfolded the hydrophobic parts of the SDS can glob onto the hydrophobic parts of the protein (which were probably hidden in the center of the protein). And then the negative heads of the SDS repel each other so the protein doesn’t try to refold. http://bit.ly/sdspageruler 

Tween-20 is a non-ionic (uncharged) detergent. And it’s considered “mild” because they don’t unfold proteins. Basically, proteins get their shape largely through interactions between the amino acids’ (protein letters)’ unique parts (side chains) and/or generic parts (backbone). Unlike the strong, covalent peptide bonds linking the letters together to form the polypeptide chain that folds up, these other interactions are non-covalent and reversible. Individually, they’re weak, but collectively they’re strong. If you think of these interactions as a sort of glue, you typically have more glue holding a protein’s shape together (intrAmolecular interactions) than you do holding proteins to other proteins or molecules (intERmolecular interactions). So those intermolecular interactions are easier to break up and milder detergents like Tween can break them up. 

Detergents like Tween-20 are great for things like preventing non-specific binding during Western blots, etc. http://bit.ly/westernblotworkflow 

In case you’re curious, the “20” in Tween-20 indicates that it has 20 ethylene oxide subunits – these are hydrophilic but NOT charged (NON-IONIC) and they’re attached to a sorbitol (a type of sugar) backbone ring. The hydrophobic part is a lauric acid (a type of fatty acid). Its relative, Tween 80 has an oleic acid tail instead. 

In addition to ionic detergents like SDS (and deoxycholate, chelate, sarkosyl, etc.) and non-ionic detergents like Tween-20 (and triton x-100, DDM, digitoxin, tween 80, etc.) there are zwitterionic detergents – these have positive and negative parts that balance each other out so there’s no net charge. An example of this is CHAPS. more good info on lab detergents: https://www.labome.com/method/Detergents-Triton-X-100-Tween-20-and-More.html 

Another common use for detergents in biology is in cell lysis (breaking open cells). Sound familiar?

Phospholipids are similar to soaps & detergents in that they are amphiphilic because they have hydrophilic heads & hydrophobic tails, but they have 2 tails, and phosphate-containing heads (phosphate is a negatively-charged group consisting of phosphorus surrounded by oxygens).⠀

They’re made from combining fatty acids with glycerol or sphingosine & phosphoric acid, then modifying the resulting phosphatidic acid to give you different head groups (e.g. ethanolamine, choline, or serine). Because they have 2 tails to coordinate, as well as different heads, they’re bulkier & it’s harder for them to coordinate w/one another to form little spheres – instead they arrange themselves into bilayer “sandwiches” with the tails in the middle. They can still form spheres (in this case called liposomes not micelles) but the center of the sphere, facing the inner layer’s hydrophilic heads, is watery because the inner layers heads face it. So it wouldn’t make a good soap, but it does make a good cell coating!⠀

It’s not just the heads of phospholipids that can vary, they can have different tails, which can influence things like their fluidity. The reason for these differences can involve how “saturated” the chains are. Saturated chains have the maximum number of hydrogens per carbon, whereas “unsaturated” chains can take more – instead of bonding to hydrogen, some of the carbons use the electron they’d usually use to bind to hydrogen to bind to their neighboring carbon even more strongly – a double bond. These double bonds introduce kinks in the chain, so they can’t pack together as tightly, so the lipids are more more flowy.⠀

In addition to the membranes surrounding the main parts of our cells, we use membranes to cordon off “rooms” inside of our cells – such as the nucleus, where DNA is held, and mitochondria, where energy is produced. The presence of such membrane-bound compartments differentiates eukaryotes (plants, animals, etc.) from prokaryotes (bacteria & archaea) which don’t have such compartments. 

Our membranes are actually chock full of proteins – at like a 3:1 protein:lipid ratio mass-wise and a 1:1 ratio surface area-wise! Cytoplasmic proteins (the ones that live in water parts of your cells) hide their hydrophobic parts in the center but membrane proteins are opposite – they hide their hydrophilic parts in the center. If they go all the way through the membrane they can form channels & pores to allow passage. Other membrane-friendly proteins don’t go through but stick to one side or the other. These can play important roles in cell signaling because they can detect changes from outside the cell and relay them throughout the cell.⠀

more about all sorts of things:  #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 or search blog: https://thebumblingbiochemist.com   


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